Starting phenix.real_space_refine on Fri Mar 6 18:58:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6red_4850/03_2026/6red_4850.cif Found real_map, /net/cci-nas-00/data/ceres_data/6red_4850/03_2026/6red_4850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6red_4850/03_2026/6red_4850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6red_4850/03_2026/6red_4850.map" model { file = "/net/cci-nas-00/data/ceres_data/6red_4850/03_2026/6red_4850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6red_4850/03_2026/6red_4850.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 116 5.16 5 C 21545 2.51 5 N 5796 2.21 5 O 6424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 245 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33899 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "P" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 895 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3609 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 456} Chain: "U" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "V" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3962 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.57, per 1000 atoms: 0.22 Number of scatterers: 33899 At special positions: 0 Unit cell: (164.16, 135, 209.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 116 16.00 P 13 15.00 Mg 5 11.99 O 6424 8.00 N 5796 7.00 C 21545 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 1.4 seconds 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8162 Finding SS restraints... Secondary structure from input PDB file: 190 helices and 0 sheets defined 52.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 54 through 68 removed outlier: 4.337A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 92 removed outlier: 3.776A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 119 removed outlier: 4.240A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'B' and resid 55 through 68 removed outlier: 3.756A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 92 removed outlier: 3.977A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 126 removed outlier: 4.483A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL B 121 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 68 removed outlier: 4.409A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 92 removed outlier: 4.394A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 126 removed outlier: 4.783A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 removed outlier: 4.220A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 92 removed outlier: 3.591A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 126 removed outlier: 4.256A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 removed outlier: 4.458A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 92 Processing helix chain 'E' and resid 95 through 126 removed outlier: 4.495A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 4.042A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 90 removed outlier: 3.569A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 94 No H-bonds generated for 'chain 'F' and resid 92 through 94' Processing helix chain 'F' and resid 95 through 126 removed outlier: 3.507A pdb=" N GLY F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 removed outlier: 3.985A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 92 removed outlier: 3.680A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 126 removed outlier: 3.571A pdb=" N LEU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA G 114 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE G 116 " --> pdb=" O SER G 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 66 removed outlier: 3.953A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 92 removed outlier: 4.336A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 124 removed outlier: 4.206A pdb=" N SER H 112 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL H 120 " --> pdb=" O PHE H 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 68 removed outlier: 3.539A pdb=" N GLY I 65 " --> pdb=" O MET I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 92 removed outlier: 4.234A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL I 74 " --> pdb=" O ALA I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 127 removed outlier: 4.235A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU I 125 " --> pdb=" O VAL I 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 removed outlier: 3.904A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS J 66 " --> pdb=" O VAL J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 92 removed outlier: 4.238A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 126 removed outlier: 4.663A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL J 120 " --> pdb=" O PHE J 116 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL J 121 " --> pdb=" O SER J 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 62 Processing helix chain 'P' and resid 66 through 84 removed outlier: 4.047A pdb=" N ASP P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU P 73 " --> pdb=" O LYS P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 93 removed outlier: 3.797A pdb=" N ARG P 88 " --> pdb=" O HIS P 84 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 109 removed outlier: 4.030A pdb=" N SER P 107 " --> pdb=" O LYS P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 128 removed outlier: 3.901A pdb=" N GLU P 123 " --> pdb=" O LYS P 119 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA P 124 " --> pdb=" O LYS P 120 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU P 128 " --> pdb=" O ALA P 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 132 No H-bonds generated for 'chain 'P' and resid 130 through 132' Processing helix chain 'P' and resid 133 through 147 removed outlier: 3.932A pdb=" N VAL P 139 " --> pdb=" O LEU P 135 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 13 Processing helix chain 'Q' and resid 15 through 29 Processing helix chain 'Q' and resid 32 through 40 removed outlier: 4.329A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN Q 40 " --> pdb=" O LYS Q 36 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 44 removed outlier: 3.783A pdb=" N ALA Q 44 " --> pdb=" O ALA Q 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 41 through 44' Processing helix chain 'R' and resid 29 through 41 removed outlier: 3.730A pdb=" N THR R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 55 Processing helix chain 'R' and resid 153 through 155 No H-bonds generated for 'chain 'R' and resid 153 through 155' Processing helix chain 'R' and resid 156 through 168 removed outlier: 3.818A pdb=" N VAL R 160 " --> pdb=" O ASP R 156 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 196 removed outlier: 3.508A pdb=" N GLU R 196 " --> pdb=" O GLU R 192 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 71 removed outlier: 3.652A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 79 Processing helix chain 'S' and resid 81 through 89 removed outlier: 4.466A pdb=" N PHE S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL S 86 " --> pdb=" O VAL S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 128 removed outlier: 3.787A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 151 removed outlier: 3.501A pdb=" N ARG S 147 " --> pdb=" O GLY S 143 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN S 149 " --> pdb=" O LYS S 145 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR S 151 " --> pdb=" O ARG S 147 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 183 Processing helix chain 'S' and resid 238 through 313 removed outlier: 3.769A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER S 272 " --> pdb=" O ALA S 268 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU S 275 " --> pdb=" O MET S 271 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU S 290 " --> pdb=" O GLY S 286 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA S 313 " --> pdb=" O ALA S 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 138 removed outlier: 4.076A pdb=" N VAL T 137 " --> pdb=" O ASN T 134 " (cutoff:3.500A) Processing helix chain 'T' and resid 156 through 160 Processing helix chain 'T' and resid 206 through 212 Processing helix chain 'T' and resid 230 through 247 removed outlier: 3.735A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) Processing helix chain 'T' and resid 265 through 280 removed outlier: 3.514A pdb=" N VAL T 269 " --> pdb=" O LYS T 265 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA T 270 " --> pdb=" O ARG T 266 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN T 271 " --> pdb=" O SER T 267 " (cutoff:3.500A) Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 295 through 315 Proline residue: T 303 - end of helix removed outlier: 4.168A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 326 through 341 removed outlier: 3.528A pdb=" N GLN T 330 " --> pdb=" O ASP T 326 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) Processing helix chain 'T' and resid 346 through 350 Processing helix chain 'T' and resid 351 through 352 No H-bonds generated for 'chain 'T' and resid 351 through 352' Processing helix chain 'T' and resid 353 through 363 Processing helix chain 'T' and resid 392 through 402 Processing helix chain 'T' and resid 410 through 415 Processing helix chain 'T' and resid 430 through 435 removed outlier: 3.879A pdb=" N ALA T 433 " --> pdb=" O VAL T 430 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA T 434 " --> pdb=" O GLY T 431 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN T 435 " --> pdb=" O SER T 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 430 through 435' Processing helix chain 'T' and resid 436 through 456 removed outlier: 3.723A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL T 442 " --> pdb=" O GLY T 438 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY T 444 " --> pdb=" O LYS T 440 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N THR T 445 " --> pdb=" O GLN T 441 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU T 448 " --> pdb=" O GLY T 444 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL T 456 " --> pdb=" O GLN T 452 " (cutoff:3.500A) Processing helix chain 'T' and resid 458 through 462 Processing helix chain 'T' and resid 469 through 482 removed outlier: 3.968A pdb=" N VAL T 473 " --> pdb=" O ALA T 469 " (cutoff:3.500A) Processing helix chain 'T' and resid 493 through 506 removed outlier: 3.635A pdb=" N ALA T 504 " --> pdb=" O ALA T 500 " (cutoff:3.500A) Processing helix chain 'T' and resid 522 through 528 Processing helix chain 'T' and resid 530 through 540 Processing helix chain 'T' and resid 543 through 556 removed outlier: 3.810A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG T 555 " --> pdb=" O LYS T 551 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS T 556 " --> pdb=" O ALA T 552 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 48 removed outlier: 3.639A pdb=" N LEU U 45 " --> pdb=" O ASP U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 73 removed outlier: 3.651A pdb=" N SER U 63 " --> pdb=" O ILE U 59 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN U 64 " --> pdb=" O GLN U 60 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ILE U 67 " --> pdb=" O SER U 63 " (cutoff:3.500A) Proline residue: U 68 - end of helix removed outlier: 3.592A pdb=" N GLU U 72 " --> pdb=" O PRO U 68 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TRP U 73 " --> pdb=" O ALA U 69 " (cutoff:3.500A) Processing helix chain 'U' and resid 74 through 77 Processing helix chain 'U' and resid 134 through 138 removed outlier: 3.940A pdb=" N VAL U 137 " --> pdb=" O ASN U 134 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE U 138 " --> pdb=" O ASP U 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 134 through 138' Processing helix chain 'U' and resid 156 through 160 removed outlier: 3.578A pdb=" N THR U 159 " --> pdb=" O GLY U 156 " (cutoff:3.500A) Processing helix chain 'U' and resid 206 through 212 Processing helix chain 'U' and resid 230 through 247 removed outlier: 3.790A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 279 Processing helix chain 'U' and resid 280 through 283 removed outlier: 3.727A pdb=" N ARG U 283 " --> pdb=" O GLY U 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 280 through 283' Processing helix chain 'U' and resid 295 through 316 Proline residue: U 303 - end of helix removed outlier: 3.793A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG U 314 " --> pdb=" O ALA U 310 " (cutoff:3.500A) Processing helix chain 'U' and resid 326 through 341 removed outlier: 3.718A pdb=" N GLN U 330 " --> pdb=" O ASP U 326 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER U 331 " --> pdb=" O LEU U 327 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL U 332 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 346 through 350 Processing helix chain 'U' and resid 351 through 352 No H-bonds generated for 'chain 'U' and resid 351 through 352' Processing helix chain 'U' and resid 353 through 363 removed outlier: 3.788A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) Processing helix chain 'U' and resid 369 through 373 Processing helix chain 'U' and resid 392 through 402 Processing helix chain 'U' and resid 412 through 416 removed outlier: 3.877A pdb=" N GLY U 416 " --> pdb=" O PHE U 413 " (cutoff:3.500A) Processing helix chain 'U' and resid 436 through 455 removed outlier: 3.590A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU U 446 " --> pdb=" O VAL U 442 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU U 449 " --> pdb=" O THR U 445 " (cutoff:3.500A) Processing helix chain 'U' and resid 456 through 460 removed outlier: 3.725A pdb=" N ALA U 460 " --> pdb=" O ALA U 457 " (cutoff:3.500A) Processing helix chain 'U' and resid 465 through 469 removed outlier: 4.385A pdb=" N ALA U 468 " --> pdb=" O ASP U 465 " (cutoff:3.500A) Processing helix chain 'U' and resid 472 through 484 removed outlier: 4.107A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) Processing helix chain 'U' and resid 493 through 501 Processing helix chain 'U' and resid 501 through 506 Processing helix chain 'U' and resid 513 through 515 No H-bonds generated for 'chain 'U' and resid 513 through 515' Processing helix chain 'U' and resid 516 through 528 removed outlier: 4.215A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA U 523 " --> pdb=" O ALA U 519 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL U 528 " --> pdb=" O VAL U 524 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 540 removed outlier: 4.056A pdb=" N LYS U 534 " --> pdb=" O PRO U 530 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 543 through 554 removed outlier: 3.899A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 48 removed outlier: 3.732A pdb=" N GLU V 47 " --> pdb=" O ALA V 44 " (cutoff:3.500A) Processing helix chain 'V' and resid 58 through 67 removed outlier: 3.683A pdb=" N ILE V 67 " --> pdb=" O SER V 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 138 removed outlier: 3.664A pdb=" N VAL V 137 " --> pdb=" O ASN V 134 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE V 138 " --> pdb=" O ASP V 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 134 through 138' Processing helix chain 'V' and resid 156 through 160 Processing helix chain 'V' and resid 206 through 213 Processing helix chain 'V' and resid 230 through 247 removed outlier: 3.943A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 250 through 253 Processing helix chain 'V' and resid 265 through 279 Processing helix chain 'V' and resid 280 through 283 Processing helix chain 'V' and resid 295 through 316 Proline residue: V 303 - end of helix removed outlier: 4.385A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 340 removed outlier: 3.549A pdb=" N GLN V 330 " --> pdb=" O ASP V 326 " (cutoff:3.500A) Processing helix chain 'V' and resid 346 through 350 removed outlier: 3.517A pdb=" N ALA V 349 " --> pdb=" O GLY V 346 " (cutoff:3.500A) Processing helix chain 'V' and resid 351 through 352 No H-bonds generated for 'chain 'V' and resid 351 through 352' Processing helix chain 'V' and resid 353 through 363 removed outlier: 3.832A pdb=" N HIS V 358 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU V 361 " --> pdb=" O LEU V 357 " (cutoff:3.500A) Processing helix chain 'V' and resid 369 through 373 removed outlier: 3.936A pdb=" N GLY V 373 " --> pdb=" O LYS V 370 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 400 Processing helix chain 'V' and resid 409 through 414 Processing helix chain 'V' and resid 438 through 454 removed outlier: 3.617A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) Processing helix chain 'V' and resid 455 through 457 No H-bonds generated for 'chain 'V' and resid 455 through 457' Processing helix chain 'V' and resid 470 through 485 removed outlier: 4.036A pdb=" N ARG V 479 " --> pdb=" O GLU V 475 " (cutoff:3.500A) Processing helix chain 'V' and resid 493 through 506 Processing helix chain 'V' and resid 513 through 515 No H-bonds generated for 'chain 'V' and resid 513 through 515' Processing helix chain 'V' and resid 516 through 528 removed outlier: 3.536A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) Processing helix chain 'V' and resid 530 through 540 removed outlier: 3.803A pdb=" N LYS V 534 " --> pdb=" O PRO V 530 " (cutoff:3.500A) Processing helix chain 'V' and resid 545 through 555 removed outlier: 4.148A pdb=" N HIS V 549 " --> pdb=" O ALA V 545 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG V 555 " --> pdb=" O LYS V 551 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 118 Processing helix chain 'X' and resid 166 through 171 Processing helix chain 'X' and resid 188 through 201 Processing helix chain 'X' and resid 216 through 229 Processing helix chain 'X' and resid 235 through 242 removed outlier: 4.114A pdb=" N GLU X 238 " --> pdb=" O LEU X 235 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG X 239 " --> pdb=" O GLY X 236 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 254 through 259 Processing helix chain 'X' and resid 260 through 275 Processing helix chain 'X' and resid 287 through 297 removed outlier: 3.737A pdb=" N THR X 291 " --> pdb=" O ILE X 287 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL X 297 " --> pdb=" O ALA X 293 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 323 Processing helix chain 'X' and resid 342 through 345 Processing helix chain 'X' and resid 348 through 355 removed outlier: 3.608A pdb=" N THR X 354 " --> pdb=" O ALA X 350 " (cutoff:3.500A) Processing helix chain 'X' and resid 365 through 370 removed outlier: 3.613A pdb=" N ALA X 369 " --> pdb=" O SER X 365 " (cutoff:3.500A) Processing helix chain 'X' and resid 393 through 421 removed outlier: 3.523A pdb=" N VAL X 399 " --> pdb=" O GLU X 395 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE X 419 " --> pdb=" O ASP X 415 " (cutoff:3.500A) Processing helix chain 'X' and resid 430 through 443 removed outlier: 3.593A pdb=" N ALA X 436 " --> pdb=" O THR X 432 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG X 441 " --> pdb=" O ARG X 437 " (cutoff:3.500A) Processing helix chain 'X' and resid 447 through 451 removed outlier: 3.864A pdb=" N GLU X 451 " --> pdb=" O GLN X 448 " (cutoff:3.500A) Processing helix chain 'X' and resid 462 through 476 Processing helix chain 'X' and resid 482 through 487 removed outlier: 3.645A pdb=" N PHE X 486 " --> pdb=" O GLU X 483 " (cutoff:3.500A) Processing helix chain 'X' and resid 491 through 508 removed outlier: 4.005A pdb=" N VAL X 495 " --> pdb=" O ASP X 491 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) Processing helix chain 'X' and resid 526 through 533 Processing helix chain 'Y' and resid 114 through 118 Processing helix chain 'Y' and resid 164 through 171 Processing helix chain 'Y' and resid 188 through 204 Processing helix chain 'Y' and resid 216 through 230 Processing helix chain 'Y' and resid 235 through 242 removed outlier: 3.601A pdb=" N GLU Y 238 " --> pdb=" O LEU Y 235 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG Y 239 " --> pdb=" O GLY Y 236 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 275 removed outlier: 5.091A pdb=" N ALA Y 262 " --> pdb=" O ARG Y 258 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LEU Y 263 " --> pdb=" O ALA Y 259 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 286 through 301 Processing helix chain 'Y' and resid 313 through 323 removed outlier: 3.730A pdb=" N LEU Y 321 " --> pdb=" O ASP Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 341 through 345 removed outlier: 3.721A pdb=" N ASP Y 344 " --> pdb=" O VAL Y 341 " (cutoff:3.500A) Processing helix chain 'Y' and resid 348 through 355 Processing helix chain 'Y' and resid 365 through 371 removed outlier: 3.611A pdb=" N LEU Y 371 " --> pdb=" O SER Y 367 " (cutoff:3.500A) Processing helix chain 'Y' and resid 388 through 412 removed outlier: 7.242A pdb=" N ALA Y 394 " --> pdb=" O ASN Y 390 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N GLU Y 395 " --> pdb=" O VAL Y 391 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N HIS Y 396 " --> pdb=" O ILE Y 392 " (cutoff:3.500A) Processing helix chain 'Y' and resid 412 through 420 removed outlier: 4.065A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE Y 419 " --> pdb=" O ASP Y 415 " (cutoff:3.500A) Processing helix chain 'Y' and resid 427 through 442 removed outlier: 4.616A pdb=" N VAL Y 433 " --> pdb=" O ASP Y 429 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS Y 438 " --> pdb=" O ALA Y 434 " (cutoff:3.500A) Processing helix chain 'Y' and resid 462 through 476 removed outlier: 3.959A pdb=" N VAL Y 473 " --> pdb=" O GLY Y 469 " (cutoff:3.500A) Processing helix chain 'Y' and resid 491 through 504 removed outlier: 3.742A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU Y 497 " --> pdb=" O LYS Y 493 " (cutoff:3.500A) Processing helix chain 'Y' and resid 505 through 508 Processing helix chain 'Y' and resid 518 through 522 removed outlier: 3.589A pdb=" N LEU Y 521 " --> pdb=" O SER Y 518 " (cutoff:3.500A) Processing helix chain 'Y' and resid 544 through 554 removed outlier: 4.175A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU Y 552 " --> pdb=" O ASP Y 548 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 118 Processing helix chain 'Z' and resid 149 through 153 removed outlier: 3.521A pdb=" N GLN Z 153 " --> pdb=" O PHE Z 150 " (cutoff:3.500A) Processing helix chain 'Z' and resid 164 through 171 removed outlier: 3.578A pdb=" N ALA Z 171 " --> pdb=" O VAL Z 167 " (cutoff:3.500A) Processing helix chain 'Z' and resid 190 through 201 Processing helix chain 'Z' and resid 216 through 229 Processing helix chain 'Z' and resid 235 through 242 removed outlier: 4.117A pdb=" N GLU Z 238 " --> pdb=" O LEU Z 235 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 254 through 259 Processing helix chain 'Z' and resid 260 through 275 removed outlier: 3.587A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 298 removed outlier: 3.855A pdb=" N THR Z 291 " --> pdb=" O ILE Z 287 " (cutoff:3.500A) Processing helix chain 'Z' and resid 313 through 323 Processing helix chain 'Z' and resid 348 through 355 removed outlier: 3.602A pdb=" N THR Z 354 " --> pdb=" O ALA Z 350 " (cutoff:3.500A) Processing helix chain 'Z' and resid 356 through 358 No H-bonds generated for 'chain 'Z' and resid 356 through 358' Processing helix chain 'Z' and resid 365 through 372 removed outlier: 3.527A pdb=" N ALA Z 369 " --> pdb=" O SER Z 365 " (cutoff:3.500A) Processing helix chain 'Z' and resid 388 through 393 Processing helix chain 'Z' and resid 393 through 412 removed outlier: 3.620A pdb=" N VAL Z 399 " --> pdb=" O GLU Z 395 " (cutoff:3.500A) Processing helix chain 'Z' and resid 413 through 420 Processing helix chain 'Z' and resid 421 through 425 removed outlier: 4.077A pdb=" N GLU Z 424 " --> pdb=" O GLY Z 421 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU Z 425 " --> pdb=" O MET Z 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 421 through 425' Processing helix chain 'Z' and resid 429 through 440 Processing helix chain 'Z' and resid 462 through 476 removed outlier: 3.690A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) Processing helix chain 'Z' and resid 482 through 486 Processing helix chain 'Z' and resid 492 through 500 removed outlier: 3.641A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) Processing helix chain 'Z' and resid 500 through 508 removed outlier: 3.579A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) Processing helix chain 'Z' and resid 509 through 511 No H-bonds generated for 'chain 'Z' and resid 509 through 511' Processing helix chain 'Z' and resid 527 through 533 1434 hydrogen bonds defined for protein. 4149 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.22 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8626 1.33 - 1.45: 5919 1.45 - 1.57: 19654 1.57 - 1.69: 21 1.69 - 1.81: 200 Bond restraints: 34420 Sorted by residual: bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.84e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.74e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.455 -0.067 1.00e-02 1.00e+04 4.54e+01 bond pdb=" C5 ATP V1001 " pdb=" N7 ATP V1001 " ideal model delta sigma weight residual 1.387 1.326 0.061 1.00e-02 1.00e+04 3.67e+01 bond pdb=" C5 ATP T1001 " pdb=" N7 ATP T1001 " ideal model delta sigma weight residual 1.387 1.331 0.056 1.00e-02 1.00e+04 3.14e+01 ... (remaining 34415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 46080 3.53 - 7.07: 519 7.07 - 10.60: 35 10.60 - 14.14: 12 14.14 - 17.67: 3 Bond angle restraints: 46649 Sorted by residual: angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 122.20 17.67 1.00e+00 1.00e+00 3.12e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 122.55 17.32 1.00e+00 1.00e+00 3.00e+02 angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 124.31 15.56 1.00e+00 1.00e+00 2.42e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 123.78 13.05 1.00e+00 1.00e+00 1.70e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 125.03 11.80 1.00e+00 1.00e+00 1.39e+02 ... (remaining 46644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.25: 20149 30.25 - 60.49: 628 60.49 - 90.74: 47 90.74 - 120.98: 0 120.98 - 151.23: 4 Dihedral angle restraints: 20828 sinusoidal: 8068 harmonic: 12760 Sorted by residual: dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -122.78 -57.22 0 5.00e+00 4.00e-02 1.31e+02 dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual -180.00 -133.09 -46.91 0 5.00e+00 4.00e-02 8.80e+01 dihedral pdb=" CA ALA Z 307 " pdb=" C ALA Z 307 " pdb=" N VAL Z 308 " pdb=" CA VAL Z 308 " ideal model delta harmonic sigma weight residual -180.00 -134.41 -45.59 0 5.00e+00 4.00e-02 8.31e+01 ... (remaining 20825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4352 0.076 - 0.152: 1053 0.152 - 0.228: 101 0.228 - 0.304: 11 0.304 - 0.380: 3 Chirality restraints: 5520 Sorted by residual: chirality pdb=" CB VAL V 180 " pdb=" CA VAL V 180 " pdb=" CG1 VAL V 180 " pdb=" CG2 VAL V 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CB ILE Y 524 " pdb=" CA ILE Y 524 " pdb=" CG1 ILE Y 524 " pdb=" CG2 ILE Y 524 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CG LEU U 202 " pdb=" CB LEU U 202 " pdb=" CD1 LEU U 202 " pdb=" CD2 LEU U 202 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 5517 not shown) Planarity restraints: 5999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.031 2.00e-02 2.50e+03 6.22e-02 3.86e+01 pdb=" C ALA Z 503 " -0.108 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.040 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA X 503 " -0.030 2.00e-02 2.50e+03 5.78e-02 3.34e+01 pdb=" C ALA X 503 " 0.100 2.00e-02 2.50e+03 pdb=" O ALA X 503 " -0.037 2.00e-02 2.50e+03 pdb=" N LYS X 504 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL Z 341 " -0.057 5.00e-02 4.00e+02 8.59e-02 1.18e+01 pdb=" N PRO Z 342 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO Z 342 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO Z 342 " -0.047 5.00e-02 4.00e+02 ... (remaining 5996 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1129 2.69 - 3.24: 32604 3.24 - 3.80: 57093 3.80 - 4.35: 76930 4.35 - 4.90: 126582 Nonbonded interactions: 294338 Sorted by model distance: nonbonded pdb=" OG1 THR X 190 " pdb="MG MG X 602 " model vdw 2.140 2.170 nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.197 2.170 nonbonded pdb=" O3G ATP U1001 " pdb="MG MG U1002 " model vdw 2.217 2.170 nonbonded pdb=" OG SER Q 15 " pdb=" OE1 GLU S 248 " model vdw 2.243 3.040 nonbonded pdb=" OG SER X 295 " pdb=" OE1 GLN X 311 " model vdw 2.268 3.040 ... (remaining 294333 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'T' selection = (chain 'U' and (resid 85 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 85 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 36 through 556) selection = chain 'Y' selection = (chain 'Z' and resid 36 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 28.530 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0191 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.121 34420 Z= 0.511 Angle : 1.043 17.672 46649 Z= 0.595 Chirality : 0.064 0.380 5520 Planarity : 0.008 0.086 5999 Dihedral : 14.607 151.228 12666 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.73 % Favored : 95.16 % Rotamer: Outliers : 0.31 % Allowed : 6.82 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.86 (0.10), residues: 4462 helix: -3.03 (0.08), residues: 2162 sheet: -1.38 (0.21), residues: 547 loop : -2.04 (0.13), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG T 146 TYR 0.024 0.003 TYR Q 52 PHE 0.034 0.003 PHE R 74 TRP 0.025 0.004 TRP Y 141 HIS 0.011 0.002 HIS R 104 Details of bonding type rmsd covalent geometry : bond 0.01201 (34420) covalent geometry : angle 1.04295 (46649) hydrogen bonds : bond 0.16415 ( 1434) hydrogen bonds : angle 7.00222 ( 4149) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 323 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 MET cc_start: -0.1054 (mmt) cc_final: -0.1572 (mtt) REVERT: G 99 LEU cc_start: 0.3804 (mt) cc_final: 0.3229 (mt) REVERT: S 183 ILE cc_start: -0.0113 (OUTLIER) cc_final: -0.0875 (mp) REVERT: T 367 LYS cc_start: 0.1617 (tptp) cc_final: 0.0687 (tttp) REVERT: T 501 VAL cc_start: -0.0756 (t) cc_final: -0.1086 (p) REVERT: U 118 MET cc_start: 0.1813 (ttt) cc_final: 0.0978 (mtt) REVERT: V 408 LEU cc_start: 0.2177 (mt) cc_final: 0.1179 (mp) REVERT: Y 52 PHE cc_start: 0.2508 (m-80) cc_final: 0.0540 (t80) REVERT: Y 64 GLU cc_start: 0.0628 (mm-30) cc_final: 0.0183 (mt-10) REVERT: Y 207 PHE cc_start: 0.2325 (m-80) cc_final: 0.1374 (m-80) REVERT: Y 386 MET cc_start: 0.2348 (mmp) cc_final: -0.1212 (mmm) REVERT: Y 422 MET cc_start: -0.2470 (ttt) cc_final: -0.3081 (mpp) REVERT: Z 80 MET cc_start: -0.0173 (mmm) cc_final: -0.0542 (ttt) REVERT: Z 251 MET cc_start: -0.1408 (ptp) cc_final: -0.1834 (mtt) REVERT: Z 411 LYS cc_start: 0.1479 (ttpt) cc_final: 0.0881 (tmtm) REVERT: Z 424 GLU cc_start: 0.3631 (pp20) cc_final: 0.2848 (tt0) REVERT: Z 486 PHE cc_start: 0.2418 (m-80) cc_final: 0.1585 (m-80) REVERT: Z 502 MET cc_start: 0.0073 (mtp) cc_final: -0.1533 (tpt) outliers start: 11 outliers final: 3 residues processed: 334 average time/residue: 0.5643 time to fit residues: 233.2458 Evaluate side-chains 209 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 205 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain V residue 137 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 1.9990 chunk 424 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 94 ASN C 87 ASN D 94 ASN E 94 ASN G 92 ASN G 94 ASN G 98 GLN J 98 GLN P 52 GLN Q 46 HIS R 38 ASN R 53 ASN R 66 HIS R 73 ASN R 83 GLN R 85 GLN R 154 GLN S 98 ASN S 116 ASN S 174 GLN S 195 ASN S 237 HIS T 386 GLN T 435 GLN ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 196 GLN U 228 GLN U 319 HIS U 386 GLN U 435 GLN U 497 GLN ** V 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 139 HIS ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 196 GLN ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 244 ASN V 278 GLN V 435 GLN V 452 GLN V 486 GLN V 497 GLN X 241 ASN X 390 ASN Y 157 GLN Y 199 ASN Y 278 GLN Y 286 ASN Y 388 ASN Y 404 GLN Z 42 GLN Z 144 HIS Z 199 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5021 r_free = 0.5021 target = 0.280523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.242111 restraints weight = 59175.526| |-----------------------------------------------------------------------------| r_work (start): 0.4692 rms_B_bonded: 2.26 r_work: 0.4630 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4523 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.4523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0629 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 34420 Z= 0.138 Angle : 0.634 9.689 46649 Z= 0.323 Chirality : 0.044 0.380 5520 Planarity : 0.005 0.060 5999 Dihedral : 7.510 153.341 4925 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.70 % Favored : 96.17 % Rotamer: Outliers : 1.77 % Allowed : 11.11 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.12), residues: 4462 helix: -1.27 (0.10), residues: 2161 sheet: -0.94 (0.22), residues: 503 loop : -1.46 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG V 347 TYR 0.024 0.002 TYR Z 340 PHE 0.030 0.002 PHE Y 288 TRP 0.008 0.001 TRP X 141 HIS 0.005 0.001 HIS U 358 Details of bonding type rmsd covalent geometry : bond 0.00298 (34420) covalent geometry : angle 0.63376 (46649) hydrogen bonds : bond 0.03845 ( 1434) hydrogen bonds : angle 4.56227 ( 4149) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 228 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 95 ILE cc_start: 0.1073 (mm) cc_final: -0.0033 (tp) REVERT: H 55 VAL cc_start: 0.6468 (m) cc_final: 0.6016 (p) REVERT: H 56 LEU cc_start: 0.4814 (mm) cc_final: 0.4431 (tp) REVERT: S 118 ASN cc_start: 0.3911 (m-40) cc_final: 0.3382 (p0) REVERT: S 223 VAL cc_start: -0.0202 (OUTLIER) cc_final: -0.0534 (t) REVERT: S 279 LYS cc_start: 0.3308 (ptmm) cc_final: 0.3074 (mmpt) REVERT: T 140 GLN cc_start: 0.4010 (mt0) cc_final: 0.2364 (tm130) REVERT: T 313 PHE cc_start: 0.2956 (m-10) cc_final: 0.2340 (m-10) REVERT: T 483 MET cc_start: 0.1276 (pp-130) cc_final: 0.0582 (ptt) REVERT: T 488 GLN cc_start: 0.3880 (OUTLIER) cc_final: 0.2873 (tp40) REVERT: U 84 LEU cc_start: -0.1321 (OUTLIER) cc_final: -0.1724 (mt) REVERT: U 118 MET cc_start: 0.2049 (ttt) cc_final: 0.1618 (mtt) REVERT: U 282 MET cc_start: -0.0969 (mmt) cc_final: -0.1360 (pmt) REVERT: V 118 MET cc_start: 0.1106 (OUTLIER) cc_final: 0.0158 (ppp) REVERT: V 134 ASN cc_start: 0.0988 (p0) cc_final: 0.0624 (p0) REVERT: V 241 HIS cc_start: 0.0583 (t70) cc_final: 0.0180 (t70) REVERT: V 258 VAL cc_start: 0.5240 (t) cc_final: 0.5019 (t) REVERT: V 321 LEU cc_start: 0.2992 (OUTLIER) cc_final: 0.1335 (mp) REVERT: X 422 MET cc_start: 0.1198 (pp-130) cc_final: -0.0437 (ptt) REVERT: X 484 MET cc_start: 0.2463 (OUTLIER) cc_final: 0.2258 (pmm) REVERT: Y 52 PHE cc_start: 0.2953 (m-80) cc_final: 0.0875 (t80) REVERT: Y 194 MET cc_start: 0.0978 (mtm) cc_final: -0.1299 (pp-130) REVERT: Y 207 PHE cc_start: 0.3605 (m-80) cc_final: 0.1982 (m-80) REVERT: Y 246 LEU cc_start: 0.0789 (OUTLIER) cc_final: 0.0372 (mt) REVERT: Y 286 ASN cc_start: 0.0327 (OUTLIER) cc_final: -0.0845 (t0) REVERT: Y 386 MET cc_start: 0.1733 (mmp) cc_final: -0.0396 (mmp) REVERT: Y 422 MET cc_start: -0.3561 (ttt) cc_final: -0.3844 (mpt) REVERT: Z 80 MET cc_start: -0.0284 (mmm) cc_final: -0.0592 (ttt) REVERT: Z 224 TYR cc_start: 0.2359 (t80) cc_final: 0.0996 (t80) REVERT: Z 251 MET cc_start: 0.0154 (ptp) cc_final: -0.0769 (mtt) REVERT: Z 348 ASP cc_start: 0.5638 (m-30) cc_final: 0.5405 (m-30) REVERT: Z 386 MET cc_start: 0.1498 (OUTLIER) cc_final: 0.1231 (ptp) REVERT: Z 422 MET cc_start: -0.0063 (tpp) cc_final: -0.0701 (tpp) REVERT: Z 424 GLU cc_start: 0.4388 (pp20) cc_final: 0.2795 (tm-30) REVERT: Z 486 PHE cc_start: 0.2683 (m-80) cc_final: 0.2229 (m-80) REVERT: Z 502 MET cc_start: -0.0932 (mtp) cc_final: -0.2522 (tpt) outliers start: 63 outliers final: 26 residues processed: 268 average time/residue: 0.5651 time to fit residues: 189.7044 Evaluate side-chains 229 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 87 VAL Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 118 MET Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 488 GLN Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 321 LEU Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 251 MET Chi-restraints excluded: chain X residue 484 MET Chi-restraints excluded: chain Y residue 246 LEU Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 286 ASN Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 386 MET Chi-restraints excluded: chain Z residue 538 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 422 optimal weight: 1.9990 chunk 307 optimal weight: 1.9990 chunk 396 optimal weight: 0.8980 chunk 243 optimal weight: 0.8980 chunk 277 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 425 optimal weight: 0.7980 chunk 384 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 114 optimal weight: 0.0370 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 98 GLN P 71 GLN S 263 ASN ** T 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 123 GLN U 228 GLN V 242 GLN X 204 HIS ** X 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 294 ASN Y 204 HIS Y 311 GLN Y 357 HIS Z 42 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5031 r_free = 0.5031 target = 0.281511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.243947 restraints weight = 59613.197| |-----------------------------------------------------------------------------| r_work (start): 0.4696 rms_B_bonded: 2.86 r_work: 0.4631 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0783 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 34420 Z= 0.121 Angle : 0.583 9.787 46649 Z= 0.295 Chirality : 0.043 0.297 5520 Planarity : 0.004 0.071 5999 Dihedral : 6.893 166.117 4921 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.65 % Favored : 96.23 % Rotamer: Outliers : 2.27 % Allowed : 13.04 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.12), residues: 4462 helix: -0.46 (0.11), residues: 2155 sheet: -0.81 (0.22), residues: 525 loop : -1.16 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 476 TYR 0.018 0.001 TYR G 102 PHE 0.023 0.001 PHE V 489 TRP 0.007 0.001 TRP Y 141 HIS 0.004 0.001 HIS T 139 Details of bonding type rmsd covalent geometry : bond 0.00260 (34420) covalent geometry : angle 0.58333 (46649) hydrogen bonds : bond 0.03545 ( 1434) hydrogen bonds : angle 4.21332 ( 4149) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 220 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 MET cc_start: -0.2825 (mtt) cc_final: -0.3222 (mmp) REVERT: C 81 MET cc_start: 0.4818 (OUTLIER) cc_final: 0.4352 (tpp) REVERT: E 95 ILE cc_start: 0.1365 (mm) cc_final: 0.0958 (mm) REVERT: H 56 LEU cc_start: 0.5001 (mm) cc_final: 0.4714 (tp) REVERT: H 60 LYS cc_start: 0.5040 (OUTLIER) cc_final: 0.4602 (tptt) REVERT: I 81 MET cc_start: -0.1346 (ppp) cc_final: -0.1860 (ppp) REVERT: J 81 MET cc_start: 0.4545 (tmm) cc_final: 0.2532 (ptm) REVERT: Q 48 ARG cc_start: 0.4411 (OUTLIER) cc_final: 0.3982 (tmm-80) REVERT: R 178 GLN cc_start: 0.4880 (OUTLIER) cc_final: 0.4570 (tt0) REVERT: S 223 VAL cc_start: -0.0495 (OUTLIER) cc_final: -0.0704 (t) REVERT: S 279 LYS cc_start: 0.3301 (ptmm) cc_final: 0.2995 (mmpt) REVERT: T 90 VAL cc_start: -0.0613 (OUTLIER) cc_final: -0.1017 (t) REVERT: T 313 PHE cc_start: 0.2489 (m-10) cc_final: 0.2080 (m-10) REVERT: T 483 MET cc_start: 0.1277 (pp-130) cc_final: 0.0405 (ptt) REVERT: T 488 GLN cc_start: 0.3869 (OUTLIER) cc_final: 0.2531 (mm-40) REVERT: U 118 MET cc_start: 0.2174 (ttt) cc_final: 0.1871 (ttt) REVERT: U 186 GLU cc_start: 0.3298 (tm-30) cc_final: 0.2576 (tp30) REVERT: U 282 MET cc_start: -0.0693 (mmt) cc_final: -0.1415 (ptm) REVERT: V 118 MET cc_start: 0.1430 (OUTLIER) cc_final: 0.0275 (ppp) REVERT: V 134 ASN cc_start: 0.1418 (p0) cc_final: 0.0806 (p0) REVERT: V 241 HIS cc_start: 0.0529 (t70) cc_final: 0.0125 (t70) REVERT: V 321 LEU cc_start: 0.3344 (OUTLIER) cc_final: 0.2225 (mp) REVERT: X 251 MET cc_start: 0.1547 (OUTLIER) cc_final: 0.1196 (mtp) REVERT: X 422 MET cc_start: 0.0769 (pp-130) cc_final: -0.0634 (ptt) REVERT: Y 52 PHE cc_start: 0.3278 (m-80) cc_final: 0.1080 (t80) REVERT: Y 166 VAL cc_start: -0.4015 (OUTLIER) cc_final: -0.4717 (t) REVERT: Y 286 ASN cc_start: -0.0678 (OUTLIER) cc_final: -0.1514 (t0) REVERT: Y 311 GLN cc_start: 0.0879 (OUTLIER) cc_final: 0.0209 (pt0) REVERT: Y 386 MET cc_start: 0.2356 (mmp) cc_final: -0.0028 (mmp) REVERT: Y 422 MET cc_start: -0.3744 (ttt) cc_final: -0.4192 (mpp) REVERT: Y 439 ILE cc_start: 0.2567 (pp) cc_final: 0.2353 (tp) REVERT: Z 224 TYR cc_start: 0.2348 (t80) cc_final: 0.0989 (t80) REVERT: Z 422 MET cc_start: 0.0029 (tpp) cc_final: -0.0651 (tpp) REVERT: Z 424 GLU cc_start: 0.4511 (pp20) cc_final: 0.3286 (tt0) REVERT: Z 486 PHE cc_start: 0.2696 (m-80) cc_final: 0.2122 (m-80) REVERT: Z 502 MET cc_start: -0.0911 (mtp) cc_final: -0.2457 (tpt) outliers start: 81 outliers final: 34 residues processed: 273 average time/residue: 0.5315 time to fit residues: 182.9545 Evaluate side-chains 244 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 197 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 141 TYR Chi-restraints excluded: chain Q residue 48 ARG Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 178 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 87 VAL Chi-restraints excluded: chain T residue 90 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 488 GLN Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain V residue 203 PHE Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 231 LYS Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 321 LEU Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 251 MET Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 286 ASN Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 311 GLN Chi-restraints excluded: chain Z residue 91 ASP Chi-restraints excluded: chain Z residue 538 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 62 optimal weight: 2.9990 chunk 360 optimal weight: 2.9990 chunk 279 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 410 optimal weight: 0.8980 chunk 321 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 423 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 409 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 ASN J 98 GLN P 76 GLN S 174 GLN T 104 GLN ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 140 GLN ** T 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 264 GLN U 405 GLN V 152 ASN ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 299 GLN ** X 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 292 GLN Z 337 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5060 r_free = 0.5060 target = 0.284295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.252291 restraints weight = 60945.878| |-----------------------------------------------------------------------------| r_work (start): 0.4783 rms_B_bonded: 2.41 r_work: 0.4718 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.4718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1276 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 34420 Z= 0.172 Angle : 0.726 12.089 46649 Z= 0.369 Chirality : 0.046 0.360 5520 Planarity : 0.006 0.080 5999 Dihedral : 7.290 141.832 4921 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.77 % Favored : 95.14 % Rotamer: Outliers : 2.83 % Allowed : 14.92 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.12), residues: 4462 helix: -0.52 (0.11), residues: 2163 sheet: -1.07 (0.23), residues: 494 loop : -1.25 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Z 120 TYR 0.101 0.003 TYR P 141 PHE 0.034 0.002 PHE U 380 TRP 0.010 0.002 TRP Y 141 HIS 0.009 0.002 HIS T 139 Details of bonding type rmsd covalent geometry : bond 0.00380 (34420) covalent geometry : angle 0.72621 (46649) hydrogen bonds : bond 0.04098 ( 1434) hydrogen bonds : angle 4.50848 ( 4149) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 231 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 123 LEU cc_start: 0.5275 (tm) cc_final: 0.4899 (pp) REVERT: H 60 LYS cc_start: 0.5003 (OUTLIER) cc_final: 0.4511 (ttmt) REVERT: I 119 LEU cc_start: 0.1676 (mm) cc_final: 0.1433 (tt) REVERT: J 81 MET cc_start: 0.4104 (tmm) cc_final: 0.2412 (ptm) REVERT: J 123 LEU cc_start: 0.1585 (tp) cc_final: 0.1245 (pp) REVERT: Q 48 ARG cc_start: 0.4504 (OUTLIER) cc_final: 0.4119 (tmm-80) REVERT: R 178 GLN cc_start: 0.4731 (OUTLIER) cc_final: 0.4310 (tp40) REVERT: S 223 VAL cc_start: -0.0993 (OUTLIER) cc_final: -0.1197 (t) REVERT: S 259 MET cc_start: 0.2511 (mmt) cc_final: 0.1126 (tmt) REVERT: T 278 GLN cc_start: -0.1750 (OUTLIER) cc_final: -0.2502 (mm-40) REVERT: T 483 MET cc_start: 0.0694 (pp-130) cc_final: 0.0054 (tpt) REVERT: V 146 ARG cc_start: 0.1979 (OUTLIER) cc_final: 0.1344 (ptm160) REVERT: V 240 ILE cc_start: 0.3638 (mt) cc_final: 0.1795 (tt) REVERT: V 241 HIS cc_start: 0.1458 (t70) cc_final: 0.0772 (t70) REVERT: V 357 LEU cc_start: 0.0013 (OUTLIER) cc_final: -0.0684 (mp) REVERT: X 194 MET cc_start: 0.0510 (OUTLIER) cc_final: -0.0595 (mpp) REVERT: X 252 ASN cc_start: 0.3662 (p0) cc_final: 0.3396 (p0) REVERT: X 253 GLU cc_start: 0.1578 (OUTLIER) cc_final: 0.1317 (mm-30) REVERT: X 260 ARG cc_start: 0.1433 (mmt-90) cc_final: 0.1146 (mtm180) REVERT: X 422 MET cc_start: 0.1068 (pp-130) cc_final: -0.0389 (ptt) REVERT: Y 52 PHE cc_start: 0.3488 (m-80) cc_final: 0.1369 (t80) REVERT: Y 422 MET cc_start: -0.3547 (ttt) cc_final: -0.4561 (mpp) REVERT: Z 43 VAL cc_start: 0.1672 (t) cc_final: 0.1334 (p) REVERT: Z 52 PHE cc_start: 0.0688 (m-80) cc_final: 0.0406 (m-80) REVERT: Z 122 MET cc_start: 0.1501 (OUTLIER) cc_final: 0.0940 (ttp) REVERT: Z 224 TYR cc_start: 0.3425 (t80) cc_final: 0.1742 (t80) REVERT: Z 251 MET cc_start: -0.0770 (OUTLIER) cc_final: -0.1352 (ptp) REVERT: Z 502 MET cc_start: -0.0613 (mtp) cc_final: -0.2327 (tpt) outliers start: 101 outliers final: 49 residues processed: 312 average time/residue: 0.5133 time to fit residues: 203.1824 Evaluate side-chains 264 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 204 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain Q residue 48 ARG Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 178 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain T residue 278 GLN Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 446 LEU Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 186 GLU Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 337 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 403 ASP Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 146 ARG Chi-restraints excluded: chain V residue 203 PHE Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 141 TRP Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 226 GLU Chi-restraints excluded: chain X residue 227 MET Chi-restraints excluded: chain X residue 243 LYS Chi-restraints excluded: chain X residue 251 MET Chi-restraints excluded: chain X residue 253 GLU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 339 VAL Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 190 THR Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 314 LEU Chi-restraints excluded: chain Y residue 340 TYR Chi-restraints excluded: chain Y residue 359 ASP Chi-restraints excluded: chain Z residue 80 MET Chi-restraints excluded: chain Z residue 91 ASP Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 251 MET Chi-restraints excluded: chain Z residue 454 THR Chi-restraints excluded: chain Z residue 538 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 128 optimal weight: 0.9980 chunk 390 optimal weight: 0.0970 chunk 256 optimal weight: 1.9990 chunk 433 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 223 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 0.0980 chunk 183 optimal weight: 0.3980 chunk 324 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 98 GLN P 71 GLN T 336 GLN ** T 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 250 GLN Z 250 GLN Z 292 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5059 r_free = 0.5059 target = 0.283838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.250819 restraints weight = 60956.031| |-----------------------------------------------------------------------------| r_work (start): 0.4772 rms_B_bonded: 2.39 r_work: 0.4707 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.4707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1131 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 34420 Z= 0.111 Angle : 0.580 12.427 46649 Z= 0.290 Chirality : 0.043 0.250 5520 Planarity : 0.004 0.047 5999 Dihedral : 6.699 150.088 4921 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.43 % Favored : 96.44 % Rotamer: Outliers : 2.61 % Allowed : 16.13 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.13), residues: 4462 helix: 0.01 (0.11), residues: 2164 sheet: -0.98 (0.23), residues: 494 loop : -1.03 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 98 TYR 0.016 0.001 TYR Z 340 PHE 0.032 0.001 PHE S 203 TRP 0.014 0.001 TRP Y 141 HIS 0.005 0.001 HIS X 144 Details of bonding type rmsd covalent geometry : bond 0.00241 (34420) covalent geometry : angle 0.58007 (46649) hydrogen bonds : bond 0.03379 ( 1434) hydrogen bonds : angle 4.05945 ( 4149) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 213 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 81 MET cc_start: -0.0009 (OUTLIER) cc_final: -0.0927 (ptt) REVERT: G 110 THR cc_start: 0.6977 (m) cc_final: 0.6533 (p) REVERT: G 123 LEU cc_start: 0.5247 (OUTLIER) cc_final: 0.4890 (pp) REVERT: J 123 LEU cc_start: 0.1206 (tp) cc_final: 0.0782 (pp) REVERT: Q 48 ARG cc_start: 0.4695 (OUTLIER) cc_final: 0.4337 (tmm-80) REVERT: S 92 PHE cc_start: 0.1194 (m-80) cc_final: 0.0787 (m-80) REVERT: S 259 MET cc_start: 0.2628 (mmt) cc_final: 0.1355 (tmt) REVERT: T 313 PHE cc_start: 0.2428 (m-10) cc_final: 0.2179 (m-10) REVERT: T 483 MET cc_start: 0.0640 (pp-130) cc_final: 0.0067 (tpt) REVERT: T 559 LEU cc_start: -0.1223 (OUTLIER) cc_final: -0.1516 (pt) REVERT: U 282 MET cc_start: 0.0105 (mmt) cc_final: -0.1219 (ptm) REVERT: U 513 ARG cc_start: 0.3411 (tpp-160) cc_final: 0.2937 (tpt170) REVERT: V 187 VAL cc_start: -0.0860 (OUTLIER) cc_final: -0.1306 (t) REVERT: V 240 ILE cc_start: 0.3787 (mt) cc_final: 0.1843 (tt) REVERT: V 241 HIS cc_start: 0.1387 (t70) cc_final: 0.0845 (t70) REVERT: V 282 MET cc_start: 0.1028 (tpt) cc_final: -0.0586 (tpt) REVERT: X 194 MET cc_start: 0.0735 (OUTLIER) cc_final: 0.0006 (mpp) REVERT: X 422 MET cc_start: 0.1050 (pp-130) cc_final: -0.0387 (ptt) REVERT: Y 52 PHE cc_start: 0.3156 (m-80) cc_final: 0.1132 (t80) REVERT: Y 422 MET cc_start: -0.3359 (ttt) cc_final: -0.4421 (mpt) REVERT: Y 501 LYS cc_start: 0.0379 (OUTLIER) cc_final: -0.0011 (mtpm) REVERT: Z 52 PHE cc_start: 0.1135 (m-80) cc_final: 0.0828 (m-80) REVERT: Z 80 MET cc_start: -0.1403 (ttt) cc_final: -0.2792 (ppp) REVERT: Z 91 ASP cc_start: 0.1388 (OUTLIER) cc_final: 0.0543 (t70) REVERT: Z 122 MET cc_start: 0.1342 (OUTLIER) cc_final: 0.0798 (ttm) REVERT: Z 224 TYR cc_start: 0.2933 (t80) cc_final: 0.1446 (t80) REVERT: Z 251 MET cc_start: -0.1205 (OUTLIER) cc_final: -0.1608 (ptp) REVERT: Z 383 THR cc_start: 0.1845 (p) cc_final: 0.1529 (t) REVERT: Z 422 MET cc_start: 0.1145 (mpp) cc_final: -0.0014 (tpp) REVERT: Z 502 MET cc_start: -0.0992 (mtp) cc_final: -0.2634 (tpt) outliers start: 93 outliers final: 50 residues processed: 285 average time/residue: 0.5419 time to fit residues: 194.0290 Evaluate side-chains 260 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 200 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain Q residue 48 ARG Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 446 LEU Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 286 ILE Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 337 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 146 ARG Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 316 THR Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 141 TRP Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 196 LEU Chi-restraints excluded: chain X residue 227 MET Chi-restraints excluded: chain X residue 243 LYS Chi-restraints excluded: chain X residue 251 MET Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 340 TYR Chi-restraints excluded: chain Y residue 501 LYS Chi-restraints excluded: chain Y residue 526 SER Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain Z residue 91 ASP Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 227 MET Chi-restraints excluded: chain Z residue 251 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 183 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 324 optimal weight: 0.1980 chunk 397 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 266 optimal weight: 0.1980 chunk 13 optimal weight: 20.0000 chunk 231 optimal weight: 0.0970 chunk 308 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 438 optimal weight: 7.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 76 GLN ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 ASN ** T 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 527 GLN U 271 GLN V 121 ASN ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 322 GLN Z 79 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5069 r_free = 0.5069 target = 0.284645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.252570 restraints weight = 60438.602| |-----------------------------------------------------------------------------| r_work (start): 0.4787 rms_B_bonded: 2.46 r_work: 0.4717 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1203 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34420 Z= 0.117 Angle : 0.592 11.171 46649 Z= 0.295 Chirality : 0.043 0.245 5520 Planarity : 0.004 0.049 5999 Dihedral : 6.632 150.797 4921 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.48 % Favored : 95.41 % Rotamer: Outliers : 2.83 % Allowed : 16.91 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.13), residues: 4462 helix: 0.21 (0.11), residues: 2171 sheet: -0.95 (0.24), residues: 474 loop : -0.93 (0.15), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 418 TYR 0.015 0.001 TYR Z 340 PHE 0.031 0.001 PHE B 82 TRP 0.011 0.001 TRP Y 141 HIS 0.005 0.001 HIS V 358 Details of bonding type rmsd covalent geometry : bond 0.00256 (34420) covalent geometry : angle 0.59246 (46649) hydrogen bonds : bond 0.03323 ( 1434) hydrogen bonds : angle 4.02021 ( 4149) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 205 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 123 LEU cc_start: 0.5161 (OUTLIER) cc_final: 0.4840 (pp) REVERT: P 74 LEU cc_start: 0.2603 (mt) cc_final: 0.2342 (mt) REVERT: R 100 VAL cc_start: -0.0248 (OUTLIER) cc_final: -0.0812 (p) REVERT: R 101 LYS cc_start: 0.3767 (mmtt) cc_final: 0.3363 (mmmm) REVERT: R 178 GLN cc_start: 0.4126 (OUTLIER) cc_final: 0.3782 (tp40) REVERT: S 92 PHE cc_start: 0.0990 (m-80) cc_final: 0.0639 (m-80) REVERT: S 259 MET cc_start: 0.2657 (mmt) cc_final: 0.1306 (tmt) REVERT: T 159 THR cc_start: -0.1641 (OUTLIER) cc_final: -0.2815 (t) REVERT: T 313 PHE cc_start: 0.2697 (m-10) cc_final: 0.2478 (m-10) REVERT: T 439 MET cc_start: 0.1530 (mtt) cc_final: 0.0917 (mtt) REVERT: T 483 MET cc_start: 0.1071 (pp-130) cc_final: 0.0432 (tpt) REVERT: T 559 LEU cc_start: -0.1197 (OUTLIER) cc_final: -0.1496 (pt) REVERT: U 282 MET cc_start: 0.0026 (mmt) cc_final: -0.1198 (ptm) REVERT: U 466 LEU cc_start: -0.4994 (OUTLIER) cc_final: -0.5250 (mp) REVERT: V 241 HIS cc_start: 0.1549 (t70) cc_final: 0.1045 (t70) REVERT: V 282 MET cc_start: 0.0997 (tpt) cc_final: -0.0803 (tpt) REVERT: X 155 THR cc_start: 0.5672 (t) cc_final: 0.5283 (m) REVERT: X 194 MET cc_start: 0.0739 (OUTLIER) cc_final: 0.0136 (mpp) REVERT: X 251 MET cc_start: 0.2144 (OUTLIER) cc_final: 0.1833 (mtp) REVERT: X 290 PHE cc_start: -0.0675 (OUTLIER) cc_final: -0.2008 (t80) REVERT: X 422 MET cc_start: 0.1032 (pp-130) cc_final: -0.0389 (ptt) REVERT: Y 52 PHE cc_start: 0.3165 (m-80) cc_final: 0.1056 (t80) REVERT: Y 68 HIS cc_start: 0.2580 (OUTLIER) cc_final: 0.2377 (t-170) REVERT: Y 422 MET cc_start: -0.3564 (ttt) cc_final: -0.4540 (mpt) REVERT: Z 52 PHE cc_start: 0.1035 (m-80) cc_final: 0.0688 (m-80) REVERT: Z 80 MET cc_start: -0.0906 (ttt) cc_final: -0.2579 (ppp) REVERT: Z 91 ASP cc_start: 0.1344 (OUTLIER) cc_final: 0.0621 (t70) REVERT: Z 122 MET cc_start: 0.1252 (OUTLIER) cc_final: 0.0854 (ttp) REVERT: Z 224 TYR cc_start: 0.3001 (t80) cc_final: 0.1460 (t80) REVERT: Z 251 MET cc_start: -0.1081 (OUTLIER) cc_final: -0.1494 (ptp) REVERT: Z 253 GLU cc_start: 0.3066 (OUTLIER) cc_final: 0.0694 (tp30) REVERT: Z 422 MET cc_start: 0.0939 (mpp) cc_final: -0.0001 (tpp) REVERT: Z 502 MET cc_start: -0.0987 (mtp) cc_final: -0.2873 (tpt) outliers start: 101 outliers final: 65 residues processed: 284 average time/residue: 0.5195 time to fit residues: 185.5311 Evaluate side-chains 268 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 189 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 178 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain T residue 159 THR Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 446 LEU Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 286 ILE Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 337 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 403 ASP Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain U residue 466 LEU Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 146 ARG Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain V residue 203 PHE Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 316 THR Chi-restraints excluded: chain V residue 489 PHE Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 141 TRP Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 227 MET Chi-restraints excluded: chain X residue 243 LYS Chi-restraints excluded: chain X residue 251 MET Chi-restraints excluded: chain X residue 290 PHE Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 68 HIS Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 190 THR Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 340 TYR Chi-restraints excluded: chain Y residue 359 ASP Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain Z residue 79 HIS Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 91 ASP Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 251 MET Chi-restraints excluded: chain Z residue 253 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 404 optimal weight: 0.7980 chunk 285 optimal weight: 2.9990 chunk 266 optimal weight: 0.8980 chunk 156 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 429 optimal weight: 2.9990 chunk 340 optimal weight: 3.9990 chunk 352 optimal weight: 0.6980 chunk 186 optimal weight: 3.9990 chunk 441 optimal weight: 0.0030 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 ASN ** T 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 79 HIS Z 79 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5074 r_free = 0.5074 target = 0.284881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.253586 restraints weight = 60511.486| |-----------------------------------------------------------------------------| r_work (start): 0.4808 rms_B_bonded: 2.45 r_work: 0.4738 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1236 moved from start: 0.5913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 34420 Z= 0.112 Angle : 0.587 11.275 46649 Z= 0.292 Chirality : 0.043 0.248 5520 Planarity : 0.004 0.047 5999 Dihedral : 6.511 141.188 4921 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.01 % Favored : 95.85 % Rotamer: Outliers : 3.00 % Allowed : 17.25 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.13), residues: 4462 helix: 0.43 (0.11), residues: 2172 sheet: -0.98 (0.24), residues: 461 loop : -0.83 (0.15), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 175 TYR 0.019 0.001 TYR V 334 PHE 0.028 0.001 PHE B 82 TRP 0.009 0.001 TRP V 73 HIS 0.003 0.001 HIS R 104 Details of bonding type rmsd covalent geometry : bond 0.00243 (34420) covalent geometry : angle 0.58717 (46649) hydrogen bonds : bond 0.03244 ( 1434) hydrogen bonds : angle 3.94522 ( 4149) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 208 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 MET cc_start: 0.2000 (tmm) cc_final: 0.1644 (tmm) REVERT: E 124 ILE cc_start: 0.1700 (OUTLIER) cc_final: 0.1408 (pt) REVERT: G 110 THR cc_start: 0.6758 (m) cc_final: 0.6454 (p) REVERT: G 123 LEU cc_start: 0.5143 (OUTLIER) cc_final: 0.4843 (pp) REVERT: J 81 MET cc_start: 0.3782 (tmm) cc_final: 0.2519 (ptm) REVERT: P 74 LEU cc_start: 0.2432 (mt) cc_final: 0.2207 (mt) REVERT: R 100 VAL cc_start: -0.0125 (OUTLIER) cc_final: -0.0397 (p) REVERT: R 178 GLN cc_start: 0.3783 (OUTLIER) cc_final: 0.3440 (tp40) REVERT: S 259 MET cc_start: 0.2630 (mmt) cc_final: 0.1305 (tmt) REVERT: T 159 THR cc_start: -0.1759 (OUTLIER) cc_final: -0.2939 (t) REVERT: T 278 GLN cc_start: -0.2364 (OUTLIER) cc_final: -0.2824 (mm-40) REVERT: T 313 PHE cc_start: 0.2977 (m-10) cc_final: 0.2777 (m-10) REVERT: T 371 GLU cc_start: -0.0008 (OUTLIER) cc_final: -0.0937 (tt0) REVERT: T 439 MET cc_start: 0.1551 (mtt) cc_final: 0.1062 (mtt) REVERT: T 483 MET cc_start: 0.0824 (pp-130) cc_final: 0.0432 (tpt) REVERT: T 559 LEU cc_start: -0.1204 (OUTLIER) cc_final: -0.1490 (pt) REVERT: U 282 MET cc_start: -0.0158 (mmt) cc_final: -0.1218 (ptm) REVERT: U 513 ARG cc_start: 0.3533 (tpp-160) cc_final: 0.3052 (tpt170) REVERT: V 146 ARG cc_start: 0.1399 (OUTLIER) cc_final: 0.1144 (ptm160) REVERT: V 241 HIS cc_start: 0.1532 (t70) cc_final: 0.1068 (t70) REVERT: V 282 MET cc_start: 0.1141 (tpt) cc_final: -0.1069 (tpt) REVERT: X 155 THR cc_start: 0.5674 (t) cc_final: 0.5313 (m) REVERT: X 194 MET cc_start: 0.0357 (OUTLIER) cc_final: -0.0217 (mpp) REVERT: X 290 PHE cc_start: -0.0529 (OUTLIER) cc_final: -0.2099 (t80) REVERT: X 422 MET cc_start: 0.1016 (pp-130) cc_final: -0.0324 (ptt) REVERT: Y 52 PHE cc_start: 0.3174 (m-80) cc_final: 0.1025 (t80) REVERT: Y 422 MET cc_start: -0.3321 (ttt) cc_final: -0.4456 (mpt) REVERT: Z 52 PHE cc_start: 0.1043 (m-80) cc_final: 0.0642 (m-80) REVERT: Z 80 MET cc_start: -0.1005 (OUTLIER) cc_final: -0.2584 (ppp) REVERT: Z 122 MET cc_start: 0.1125 (OUTLIER) cc_final: 0.0791 (ttp) REVERT: Z 224 TYR cc_start: 0.2988 (t80) cc_final: 0.1494 (t80) REVERT: Z 251 MET cc_start: -0.1105 (OUTLIER) cc_final: -0.1620 (ptp) REVERT: Z 253 GLU cc_start: 0.3041 (OUTLIER) cc_final: 0.0688 (tp30) REVERT: Z 308 VAL cc_start: -0.0148 (OUTLIER) cc_final: -0.0496 (t) REVERT: Z 422 MET cc_start: 0.0978 (mpp) cc_final: 0.0483 (tpp) REVERT: Z 502 MET cc_start: -0.1490 (mtp) cc_final: -0.3126 (tpt) outliers start: 107 outliers final: 63 residues processed: 289 average time/residue: 0.5241 time to fit residues: 191.0071 Evaluate side-chains 270 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 191 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 178 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain T residue 159 THR Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain T residue 278 GLN Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 371 GLU Chi-restraints excluded: chain T residue 446 LEU Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 186 GLU Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 286 ILE Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 337 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 403 ASP Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 146 ARG Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain V residue 203 PHE Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 316 THR Chi-restraints excluded: chain V residue 489 PHE Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 141 TRP Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 196 LEU Chi-restraints excluded: chain X residue 243 LYS Chi-restraints excluded: chain X residue 290 PHE Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 340 TYR Chi-restraints excluded: chain Y residue 359 ASP Chi-restraints excluded: chain Y residue 526 SER Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain Z residue 80 MET Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 251 MET Chi-restraints excluded: chain Z residue 253 GLU Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 538 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 86 optimal weight: 7.9990 chunk 167 optimal weight: 0.4980 chunk 29 optimal weight: 8.9990 chunk 339 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 366 optimal weight: 0.0670 chunk 390 optimal weight: 3.9990 chunk 242 optimal weight: 0.0570 chunk 267 optimal weight: 0.9980 chunk 302 optimal weight: 0.0570 overall best weight: 0.3354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 ASN ** T 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 264 GLN ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 299 GLN X 294 ASN Y 250 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5073 r_free = 0.5073 target = 0.284575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.252636 restraints weight = 60821.172| |-----------------------------------------------------------------------------| r_work (start): 0.4805 rms_B_bonded: 2.42 r_work: 0.4736 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1152 moved from start: 0.6080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 34420 Z= 0.101 Angle : 0.569 12.439 46649 Z= 0.280 Chirality : 0.042 0.198 5520 Planarity : 0.004 0.048 5999 Dihedral : 6.246 130.523 4921 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.92 % Favored : 95.94 % Rotamer: Outliers : 2.36 % Allowed : 18.29 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.13), residues: 4462 helix: 0.68 (0.12), residues: 2169 sheet: -0.71 (0.25), residues: 444 loop : -0.72 (0.15), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 98 TYR 0.025 0.001 TYR V 334 PHE 0.028 0.001 PHE G 82 TRP 0.009 0.001 TRP V 73 HIS 0.002 0.001 HIS X 144 Details of bonding type rmsd covalent geometry : bond 0.00216 (34420) covalent geometry : angle 0.56892 (46649) hydrogen bonds : bond 0.03063 ( 1434) hydrogen bonds : angle 3.80004 ( 4149) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 201 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 MET cc_start: -0.3452 (mtt) cc_final: -0.3963 (tpp) REVERT: C 81 MET cc_start: 0.5482 (ppp) cc_final: 0.4950 (ppp) REVERT: D 61 MET cc_start: 0.4309 (mmt) cc_final: 0.3969 (tmm) REVERT: E 95 ILE cc_start: 0.2605 (mp) cc_final: 0.2354 (mm) REVERT: J 81 MET cc_start: 0.3967 (tmm) cc_final: 0.2657 (ptm) REVERT: R 100 VAL cc_start: -0.0327 (OUTLIER) cc_final: -0.0883 (p) REVERT: R 101 LYS cc_start: 0.3389 (mmtt) cc_final: 0.3065 (mmmt) REVERT: R 178 GLN cc_start: 0.3753 (OUTLIER) cc_final: 0.3415 (tp40) REVERT: S 315 MET cc_start: 0.2081 (pmm) cc_final: 0.1328 (pmt) REVERT: T 483 MET cc_start: 0.0993 (pp-130) cc_final: 0.0710 (tpt) REVERT: T 559 LEU cc_start: -0.1136 (OUTLIER) cc_final: -0.1422 (pt) REVERT: U 282 MET cc_start: -0.0380 (mmt) cc_final: -0.1133 (ptm) REVERT: U 321 LEU cc_start: 0.0384 (OUTLIER) cc_final: 0.0134 (mt) REVERT: U 411 GLU cc_start: 0.0284 (OUTLIER) cc_final: -0.1328 (mt-10) REVERT: U 483 MET cc_start: 0.2470 (OUTLIER) cc_final: 0.0882 (tmm) REVERT: V 118 MET cc_start: 0.1256 (ptp) cc_final: 0.1052 (ptm) REVERT: V 126 HIS cc_start: 0.2735 (p90) cc_final: 0.2300 (p90) REVERT: V 241 HIS cc_start: 0.1507 (t70) cc_final: 0.1066 (t70) REVERT: V 255 VAL cc_start: 0.0857 (OUTLIER) cc_final: -0.0226 (p) REVERT: V 282 MET cc_start: 0.0951 (tpt) cc_final: -0.1149 (tpt) REVERT: X 155 THR cc_start: 0.5644 (t) cc_final: 0.5290 (m) REVERT: X 194 MET cc_start: 0.0322 (OUTLIER) cc_final: -0.0223 (mpp) REVERT: X 290 PHE cc_start: -0.0880 (OUTLIER) cc_final: -0.2423 (t80) REVERT: X 422 MET cc_start: 0.1119 (pp-130) cc_final: -0.0273 (ptt) REVERT: Y 52 PHE cc_start: 0.2958 (m-80) cc_final: 0.0911 (t80) REVERT: Y 422 MET cc_start: -0.3306 (ttt) cc_final: -0.4411 (mpp) REVERT: Z 52 PHE cc_start: 0.1026 (m-80) cc_final: 0.0606 (m-80) REVERT: Z 80 MET cc_start: -0.0568 (ttt) cc_final: -0.2277 (ppp) REVERT: Z 122 MET cc_start: 0.1109 (OUTLIER) cc_final: 0.0808 (ttp) REVERT: Z 224 TYR cc_start: 0.2650 (t80) cc_final: 0.1662 (t80) REVERT: Z 251 MET cc_start: -0.1168 (OUTLIER) cc_final: -0.1758 (ptp) REVERT: Z 422 MET cc_start: 0.0887 (mpp) cc_final: 0.0621 (tpp) REVERT: Z 486 PHE cc_start: 0.1845 (m-80) cc_final: 0.0823 (m-80) REVERT: Z 488 MET cc_start: 0.0737 (mmt) cc_final: -0.0504 (ptm) REVERT: Z 502 MET cc_start: -0.1370 (mtp) cc_final: -0.2936 (tpt) outliers start: 84 outliers final: 49 residues processed: 260 average time/residue: 0.5339 time to fit residues: 174.4301 Evaluate side-chains 250 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 190 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 178 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 186 GLU Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 286 ILE Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 321 LEU Chi-restraints excluded: chain U residue 337 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 403 ASP Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain U residue 466 LEU Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain V residue 203 PHE Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 316 THR Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 141 TRP Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 290 PHE Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 194 MET Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 227 MET Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 340 TYR Chi-restraints excluded: chain Y residue 359 ASP Chi-restraints excluded: chain Y residue 526 SER Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 251 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 115 optimal weight: 3.9990 chunk 351 optimal weight: 0.8980 chunk 182 optimal weight: 9.9990 chunk 278 optimal weight: 0.9980 chunk 438 optimal weight: 7.9990 chunk 241 optimal weight: 0.5980 chunk 257 optimal weight: 1.9990 chunk 246 optimal weight: 0.9990 chunk 230 optimal weight: 4.9990 chunk 259 optimal weight: 0.9990 chunk 408 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 ASN ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 ASN ** T 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 GLN X 204 HIS ** X 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5080 r_free = 0.5080 target = 0.285300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.255071 restraints weight = 61062.182| |-----------------------------------------------------------------------------| r_work (start): 0.4812 rms_B_bonded: 2.42 r_work: 0.4741 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1340 moved from start: 0.6584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34420 Z= 0.128 Angle : 0.636 14.856 46649 Z= 0.313 Chirality : 0.044 0.238 5520 Planarity : 0.004 0.047 5999 Dihedral : 6.517 123.421 4921 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.73 % Favored : 95.14 % Rotamer: Outliers : 2.38 % Allowed : 18.37 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.13), residues: 4462 helix: 0.57 (0.12), residues: 2157 sheet: -1.21 (0.24), residues: 465 loop : -0.75 (0.15), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG T 364 TYR 0.066 0.002 TYR Y 487 PHE 0.050 0.002 PHE R 70 TRP 0.010 0.001 TRP P 58 HIS 0.005 0.001 HIS Y 204 Details of bonding type rmsd covalent geometry : bond 0.00282 (34420) covalent geometry : angle 0.63602 (46649) hydrogen bonds : bond 0.03346 ( 1434) hydrogen bonds : angle 3.95194 ( 4149) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 220 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 MET cc_start: 0.2096 (tmm) cc_final: 0.1553 (tmm) REVERT: C 61 MET cc_start: -0.3349 (mtt) cc_final: -0.3777 (tpp) REVERT: C 81 MET cc_start: 0.5619 (ppp) cc_final: 0.5279 (ppp) REVERT: G 110 THR cc_start: 0.6791 (m) cc_final: 0.6496 (p) REVERT: R 178 GLN cc_start: 0.3780 (OUTLIER) cc_final: 0.3422 (tp40) REVERT: T 278 GLN cc_start: -0.2482 (OUTLIER) cc_final: -0.2871 (mm-40) REVERT: T 483 MET cc_start: 0.1024 (pp-130) cc_final: 0.0709 (tpt) REVERT: T 559 LEU cc_start: -0.1091 (OUTLIER) cc_final: -0.1366 (pt) REVERT: U 282 MET cc_start: -0.0072 (mmt) cc_final: -0.1083 (ptm) REVERT: U 411 GLU cc_start: 0.0690 (OUTLIER) cc_final: -0.1102 (mt-10) REVERT: V 126 HIS cc_start: 0.3151 (p90) cc_final: 0.2872 (p90) REVERT: V 240 ILE cc_start: 0.4088 (mt) cc_final: 0.3438 (pt) REVERT: V 241 HIS cc_start: 0.1622 (t70) cc_final: 0.1053 (t70) REVERT: V 282 MET cc_start: 0.1256 (tpt) cc_final: -0.0886 (tpt) REVERT: X 155 THR cc_start: 0.5952 (t) cc_final: 0.5586 (m) REVERT: X 194 MET cc_start: 0.0234 (OUTLIER) cc_final: -0.0356 (mpp) REVERT: X 290 PHE cc_start: -0.0851 (OUTLIER) cc_final: -0.2542 (t80) REVERT: X 422 MET cc_start: 0.1374 (pp-130) cc_final: -0.0249 (ptt) REVERT: Y 52 PHE cc_start: 0.3308 (m-80) cc_final: 0.1093 (t80) REVERT: Y 422 MET cc_start: -0.2886 (ttt) cc_final: -0.4335 (mpt) REVERT: Z 43 VAL cc_start: 0.1633 (t) cc_final: 0.1368 (p) REVERT: Z 80 MET cc_start: -0.0534 (ttt) cc_final: -0.2403 (ppp) REVERT: Z 213 VAL cc_start: 0.0514 (OUTLIER) cc_final: -0.0781 (p) REVERT: Z 224 TYR cc_start: 0.3102 (t80) cc_final: 0.1539 (t80) REVERT: Z 251 MET cc_start: -0.0929 (mmt) cc_final: -0.1980 (ptp) REVERT: Z 422 MET cc_start: 0.1246 (mpp) cc_final: 0.0915 (tpp) REVERT: Z 488 MET cc_start: 0.0989 (mmt) cc_final: -0.0572 (ptm) REVERT: Z 502 MET cc_start: -0.1252 (mtp) cc_final: -0.3091 (tpt) outliers start: 85 outliers final: 58 residues processed: 285 average time/residue: 0.5686 time to fit residues: 202.1553 Evaluate side-chains 275 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 210 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 178 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 210 ILE Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain T residue 278 GLN Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 186 GLU Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 286 ILE Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 337 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 403 ASP Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain V residue 203 PHE Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 489 PHE Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 141 TRP Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 290 PHE Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 58 SER Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 194 MET Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 227 MET Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 340 TYR Chi-restraints excluded: chain Y residue 359 ASP Chi-restraints excluded: chain Y residue 526 SER Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 213 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 267 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 85 optimal weight: 5.9990 chunk 190 optimal weight: 0.5980 chunk 404 optimal weight: 0.6980 chunk 412 optimal weight: 7.9990 chunk 242 optimal weight: 0.9990 chunk 380 optimal weight: 0.9980 chunk 305 optimal weight: 0.7980 chunk 287 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 ASN T 486 GLN ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5089 r_free = 0.5089 target = 0.286213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.256497 restraints weight = 61280.083| |-----------------------------------------------------------------------------| r_work (start): 0.4829 rms_B_bonded: 2.41 r_work: 0.4757 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1337 moved from start: 0.6860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34420 Z= 0.118 Angle : 0.624 15.092 46649 Z= 0.306 Chirality : 0.043 0.225 5520 Planarity : 0.004 0.048 5999 Dihedral : 6.369 114.361 4921 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.30 % Favored : 95.56 % Rotamer: Outliers : 2.05 % Allowed : 18.91 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.13), residues: 4462 helix: 0.67 (0.12), residues: 2153 sheet: -1.25 (0.24), residues: 468 loop : -0.73 (0.15), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG V 146 TYR 0.021 0.001 TYR V 334 PHE 0.025 0.002 PHE G 82 TRP 0.009 0.001 TRP V 73 HIS 0.006 0.001 HIS U 126 Details of bonding type rmsd covalent geometry : bond 0.00258 (34420) covalent geometry : angle 0.62405 (46649) hydrogen bonds : bond 0.03278 ( 1434) hydrogen bonds : angle 3.92854 ( 4149) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 207 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.1298 (ppp) cc_final: 0.1038 (ppp) REVERT: B 81 MET cc_start: 0.2134 (tmm) cc_final: 0.1571 (tmm) REVERT: C 61 MET cc_start: -0.3463 (mtt) cc_final: -0.3849 (tpp) REVERT: C 81 MET cc_start: 0.5603 (ppp) cc_final: 0.5291 (ppp) REVERT: F 61 MET cc_start: -0.0835 (mmt) cc_final: -0.2628 (mmm) REVERT: G 110 THR cc_start: 0.6762 (m) cc_final: 0.6451 (p) REVERT: G 123 LEU cc_start: 0.5163 (tm) cc_final: 0.4565 (pp) REVERT: J 61 MET cc_start: 0.2404 (tmt) cc_final: 0.1824 (tmm) REVERT: P 146 LEU cc_start: 0.6832 (OUTLIER) cc_final: 0.6593 (mm) REVERT: R 178 GLN cc_start: 0.3887 (OUTLIER) cc_final: 0.3508 (tp40) REVERT: T 118 MET cc_start: -0.0656 (ttp) cc_final: -0.2366 (mtp) REVERT: T 278 GLN cc_start: -0.2493 (OUTLIER) cc_final: -0.2880 (mm-40) REVERT: T 371 GLU cc_start: 0.0092 (OUTLIER) cc_final: -0.1038 (mm-30) REVERT: T 483 MET cc_start: 0.0858 (pp-130) cc_final: 0.0569 (tpt) REVERT: T 559 LEU cc_start: -0.0965 (OUTLIER) cc_final: -0.1248 (pt) REVERT: U 186 GLU cc_start: 0.4594 (OUTLIER) cc_final: 0.4141 (mm-30) REVERT: U 282 MET cc_start: -0.0318 (mmt) cc_final: -0.1056 (ptm) REVERT: U 411 GLU cc_start: 0.0993 (OUTLIER) cc_final: -0.0745 (mt-10) REVERT: V 126 HIS cc_start: 0.3242 (p90) cc_final: 0.2859 (p90) REVERT: V 146 ARG cc_start: 0.2049 (mmp80) cc_final: 0.0562 (mmt-90) REVERT: V 240 ILE cc_start: 0.4053 (mt) cc_final: 0.3462 (pt) REVERT: V 241 HIS cc_start: 0.1746 (t70) cc_final: 0.1174 (t70) REVERT: V 282 MET cc_start: 0.1289 (tpt) cc_final: -0.0890 (tpt) REVERT: X 155 THR cc_start: 0.5954 (t) cc_final: 0.5573 (m) REVERT: X 194 MET cc_start: 0.0220 (OUTLIER) cc_final: -0.0355 (mpp) REVERT: X 290 PHE cc_start: -0.0844 (OUTLIER) cc_final: -0.2512 (t80) REVERT: X 422 MET cc_start: 0.1193 (pp-130) cc_final: -0.0413 (ptt) REVERT: Y 52 PHE cc_start: 0.3354 (m-80) cc_final: 0.1079 (t80) REVERT: Y 422 MET cc_start: -0.2986 (ttt) cc_final: -0.4302 (mpt) REVERT: Z 43 VAL cc_start: 0.1659 (t) cc_final: 0.1444 (p) REVERT: Z 80 MET cc_start: -0.0525 (ttt) cc_final: -0.2406 (ppp) REVERT: Z 213 VAL cc_start: 0.0720 (OUTLIER) cc_final: -0.0639 (p) REVERT: Z 224 TYR cc_start: 0.3186 (t80) cc_final: 0.1649 (t80) REVERT: Z 251 MET cc_start: -0.0557 (mmt) cc_final: -0.1804 (pp-130) REVERT: Z 422 MET cc_start: 0.1149 (mpp) cc_final: 0.0298 (tpp) REVERT: Z 486 PHE cc_start: 0.1953 (m-80) cc_final: 0.1073 (m-80) REVERT: Z 488 MET cc_start: 0.0812 (mmt) cc_final: -0.0638 (ptm) REVERT: Z 502 MET cc_start: -0.1492 (mtp) cc_final: -0.2726 (tpt) outliers start: 73 outliers final: 53 residues processed: 262 average time/residue: 0.6006 time to fit residues: 195.2607 Evaluate side-chains 260 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 197 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 178 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 210 ILE Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain T residue 278 GLN Chi-restraints excluded: chain T residue 371 GLU Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 123 GLN Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 186 GLU Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 286 ILE Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 337 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 383 ILE Chi-restraints excluded: chain U residue 403 ASP Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 453 TYR Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain V residue 203 PHE Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 141 TRP Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 290 PHE Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 325 ILE Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 58 SER Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 194 MET Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 227 MET Chi-restraints excluded: chain Y residue 294 ASN Chi-restraints excluded: chain Y residue 340 TYR Chi-restraints excluded: chain Y residue 359 ASP Chi-restraints excluded: chain Y residue 526 SER Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain Z residue 91 ASP Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 213 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 368 optimal weight: 0.7980 chunk 270 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 242 optimal weight: 0.0470 chunk 15 optimal weight: 1.9990 chunk 265 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 325 optimal weight: 3.9990 chunk 247 optimal weight: 2.9990 chunk 418 optimal weight: 0.8980 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 ASN ** T 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 322 GLN Z 292 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5092 r_free = 0.5092 target = 0.286486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.257458 restraints weight = 60850.058| |-----------------------------------------------------------------------------| r_work (start): 0.4833 rms_B_bonded: 2.40 r_work: 0.4763 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1371 moved from start: 0.7189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 34420 Z= 0.121 Angle : 0.633 15.173 46649 Z= 0.313 Chirality : 0.043 0.239 5520 Planarity : 0.004 0.050 5999 Dihedral : 6.315 108.843 4920 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.80 % Favored : 95.07 % Rotamer: Outliers : 2.22 % Allowed : 19.05 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.13), residues: 4462 helix: 0.64 (0.12), residues: 2166 sheet: -1.32 (0.24), residues: 463 loop : -0.75 (0.15), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG V 146 TYR 0.021 0.001 TYR V 334 PHE 0.046 0.002 PHE R 70 TRP 0.010 0.001 TRP P 58 HIS 0.005 0.001 HIS U 126 Details of bonding type rmsd covalent geometry : bond 0.00266 (34420) covalent geometry : angle 0.63346 (46649) hydrogen bonds : bond 0.03322 ( 1434) hydrogen bonds : angle 3.97987 ( 4149) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11432.38 seconds wall clock time: 195 minutes 47.53 seconds (11747.53 seconds total)